We investigate properties of Ganymede’s FUV auroral ovals using spectral images acquired during two visits in 2010 and 2011 with Hubble’s Space Telescope Imaging Spectrograph (HST/STIS campaign 12244) when Ganymede was at eastern elongation. We analyze the variability of structure and brightness of the auroral ovals as a function of magnetic latitude. The investigation of the aurora is a diagnostic tool to gain a better understanding of Ganymede’s intrinsic magnetic field, as the properties of the aurora on Ganymede are likely to be controlled by the interaction between the moon and the surrounding Jovian magnetospheric plasma. The variability which we find consists of both, spatial inhomogeneities on the moon disc and temporal variation as a function of Ganymede’s position within the current sheet of Jupiter’s magnetosphere. The comparison of our results with those from previous observations reveals an additional temporal variability as the brightness properties vary for different elongations in different periods.